Molecular dynamics simulations of biomolecules, proteins especially, have emerged as an important tool in the study of the conformational change, flexibility, and dynamics. These simulations, especially when combined with virtual screening, have been a tool in drug discovery. Herein, we cover the basics of molecular dynamics simulation, in the hopes that a reader would be able to intelligently conduct a simulation of their favorite protein(s), analyze the results in order to make hypotheses about the links between protein dynamics and conformation. We also discuss the integration between molecular dynamics and virtual screening, so that a reader could use the results of simulations to perform virtual screening for lead identification. Finally, we review several case studies to show what sort of information can be gained by simulation of biomedically interesting proteins, and how that may impact drug discovery, as well as a discussion of some areas in which simulation may prove more useful in the near future.